Regarding the door that the covies sealed and keyes then opened in 343 Guilty Spark.

As has been mentioned, the flood were already out and about doing their thing, so why seal the door?

Perhaps it wasn't to keep something in, but to keep something out. Now if I remember correctly, weren't the gun placements and shields set up in a way that appeared to be wanting to keep something out, rather than keep something in?

On the top when u first enter the complex there are no defences, if u wanted to keep something in, that would be where u would place your last line of defence as it were, but if u think of trying to keep something out, then that same area is undefendable, its too open, so they move their first line to where it is after u get off the lift, because any enemy coming in would be concentrated in a smaller space and easier to take out.

All gun placements are pointed at the doors you go through (coming from outside, going in). As are the shields.

Perhaps there was something important in that facility and the covenant knew that if they wanted to keep it, they'd have to fight for it.

Keyes' stated reason for going down there in the first place was to retrieve an arms cache. In Halo: The Flood, however, we learn that it's a cache of Covenant weapons that were brought there to help guard the place. It wouldn't be that unusual for the Elites, Jackals, and Grunts to not know all of the specifics of the contents of the structure they've been sent to guard.